Define similarity in a non-biological and biological sense when provided with two strings of letters.

Quantify the similarity between two gene/protein sequences.

Explain how a substitution matrix is used to quantify similarity.

Calculate amino acid similarity scores using a scoring matrix.

Demonstrate how to access genomic data (e.g., from NCBI nucleotide and protein databases).

Demonstrate how to use bioinformatics tools to analyze genomic data (e.g., BLASTP), explain a simplified BLAST search algorithm including how similarity is used to perform a BLAST search, and how to evaluate the results of a BLAST search.

Create a nearest-neighbor distance matrix.

Create a multiple sequence alignment using a nearest-neighbor distance matrix and a phylogram based on similarity of amino acid sequences.

Locate the coding sequence, flanking sequence, protein product, and characteristics of a given gene from the Saccharomyces Genome Database (https://www.yeastgenome.org/).

Design and defend the design of guide RNA and single stranded template for DNA repair in CRISPR/Cas9 gene editing studies to generate Saccharomyces cerevisiae auxotrophic mutants.

Week 3-4: Cloning

Describe the qualities of the vector, pML104, that allow replication and selection in bacteria and yeast as well as allow expression of necessary factors in CRISPR/Cas9 genome editing, including Cas9 and sgRNA.

Describe the rationale of and perform procedures necessary for cloning a small cassette (i.e., sgRNA gene) into a vector (i.e., pML104) including; restriction digest, annealing of DNA strands, removal of 5’ phosphates, ligation, and transformation.

Recognize and design appropriate controls for cloning procedures such as ligation and transformation.

Week 5: Screening clones

Describe the method of polymerase chain reaction (PCR), including the rationale for essential components of a reaction mixture and thermal-cycling conditions.

Locate the binding sites of and design primers for PCR, then report the expected size of the amplification product.

Describe and perform isolation of plasmid DNA from E. coli.

Week 6: Selection of clones and transformation of yeast

Describe the rationale for and perform procedures to transform yeast, including the essential components of a transformation mixture and conditions necessary for transformation.

Describe the basic conditions required for cultivating yeast.

Describe the rationale for and perform agarose gel electrophoresis of a given size of DNA.

Communicate science to peers through maintenance of a laboratory notebook, verbal communication with group members, and writing of a formal laboratory report written in a format acceptable for journal publication.

Troubleshoot scientific protocols by identifying procedures that are prone to error, comparing recommended protocols to actual procedure, and using positive and negative controls to narrow the location of a potential error.

Students will be able to evaluate the strengths and weaknesses of data.

Students will be able to employ prior knowledge in formulating a biological research question or hypothesis.

Students will be able to distinguish a research question from a testable hypothesis.

Students will recognize that the following are essential elements in experimental design: identifying gaps in prior knowledge, picking an appropriate approach (ex. experimental tools and controls) for testing a hypothesis, and reproducibility and repeatability.

Students will be able to identify appropriate experimental tools, approaches and controls to use in testing a hypothesis.

Students will be able to accurately explain why an experimental approach they have selected is a good choice for testing a particular hypothesis.

Students will be able to discuss whether experimental outcomes support or fail to support a particular hypothesis, and in the case of the latter, discuss possible reasons why.

Apply findings from each week's lesson to make predictions and informed hypotheses about the next week's lesson.

Keep a detailed laboratory notebook.

Write and peer-edit the sections of a scientific paper, and collaboratively write an entire lab report in the form of a scientific research paper.

Search for, find, and read scientific research papers.

Work together as a team to conduct experiments.

Connect findings and ideas from each week's lesson to get a broader understanding of how plants will respond to higher levels of CO2 (e.g., stomatal density, photosynthetic/respiratory rates, foliar protein concentrations, growth, and resource allocation).

Note: Additional, more specific objectives are included with each of the four lessons (Supporting Files S1-S4)

Students will name and describe the salient features and cellular tasks for each stage of cell division.

Students will predict the relative durations of the stages of cell division using prior knowledge and facts from assigned readings.

Students will describe the relationship between duration of each stage of cell division and the frequency of cells present in each stage of cell division counted in a random sample of images of pluripotent stem cells.

Students will identify the stages of cell division present in research-quality images of human pluripotent stem cells in various stages of cell division.

Students will quantify, analyze and summarize data on the prevalence of cells at different stages of cell division in randomly sampled cell populations.

formulate a hypothesis and design an experiment with the proper controls.

describe the steps involved in the zebrafish wounding assay (treating zebrafish embryos with drugs or control substances, wounding the embryo, staining the embryo, and counting neutrophils near the wound).

summarize results into a figure and write a descriptive figure legend.

perform appropriate statistical analysis.

interpret results in a discussion that draws connections between the cytoskeleton and cell migration.

put data into context by appropriately using information from journal articles in the introduction and discussion of a lab report.